What i see is that you have a hold on and you didn't turn it off or designate a new plotting window/figure. Such athat depending on the order of running these sections it'll probably plot within the same window. Good practice if you want a new plot is to use the function figure() to generate a new plotting window and work with axes and figure handles. the function figure can take in a figure handle or a number to designate the window number. figure(1) or figure(100) will open up a new figure with that window number assigned it.
below is a snippet of code to show what is happening as well as how to assign and designate figure and axes handles to designate where plots go.
%here showing the stacking of plots due to the "hold on"
figure(1) ; %open new figure
plot(randi(10,1,10))
hold on
%%doing other stuff here
plot(1:10,1:10)
legend('first plot','second plot')
%forcing plots into new figures, and pointing the plots into which
%figure/axes to plot into
hfig2 = figure(2); %generate handle for figure(2)
hax2 = axes(hfig2); %assign handle for axes in figure(2)
hfig3 = figure(3);
hax3 = axes(hfig3);
%put plot specifically into figure(2)
plot(hax2,randi(10,1,10))
%put plot specifically into figure(3)
plot(hax3,1:10,1:10)
